{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T03:56:00Z","timestamp":1790740560398,"version":"4.1.0"},"reference-count":34,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Science and Technology of China","award":["2020YFA0907100"],"award-info":[{"award-number":["2020YFA0907100"]}]},{"name":"Ministry of Science and Technology of China","award":["31961133019"],"award-info":[{"award-number":["31961133019"]}]},{"name":"Ministry of Science and Technology of China","award":["32071412"],"award-info":[{"award-number":["32071412"]}]},{"name":"Ministry of Science and Technology of China","award":["32171428"],"award-info":[{"award-number":["32171428"]}]},{"name":"Ministry of Science and Technology of China","award":["XDB0480000"],"award-info":[{"award-number":["XDB0480000"]}]},{"name":"Natural Science Foundation of China","award":["2020YFA0907100"],"award-info":[{"award-number":["2020YFA0907100"]}]},{"name":"Natural Science Foundation of China","award":["31961133019"],"award-info":[{"award-number":["31961133019"]}]},{"name":"Natural Science Foundation of China","award":["32071412"],"award-info":[{"award-number":["32071412"]}]},{"name":"Natural Science Foundation of China","award":["32171428"],"award-info":[{"award-number":["32171428"]}]},{"name":"Natural Science Foundation of China","award":["XDB0480000"],"award-info":[{"award-number":["XDB0480000"]}]},{"name":"Chinese Academy of Sciences","award":["2020YFA0907100"],"award-info":[{"award-number":["2020YFA0907100"]}]},{"name":"Chinese Academy of Sciences","award":["31961133019"],"award-info":[{"award-number":["31961133019"]}]},{"name":"Chinese Academy of Sciences","award":["32071412"],"award-info":[{"award-number":["32071412"]}]},{"name":"Chinese Academy of Sciences","award":["32171428"],"award-info":[{"award-number":["32171428"]}]},{"name":"Chinese Academy of Sciences","award":["XDB0480000"],"award-info":[{"award-number":["XDB0480000"]}]},{"name":"CAS Youth Interdisciplinary Team","award":["2020YFA0907100"],"award-info":[{"award-number":["2020YFA0907100"]}]},{"name":"CAS Youth Interdisciplinary Team","award":["31961133019"],"award-info":[{"award-number":["31961133019"]}]},{"name":"CAS Youth Interdisciplinary Team","award":["32071412"],"award-info":[{"award-number":["32071412"]}]},{"name":"CAS Youth Interdisciplinary Team","award":["32171428"],"award-info":[{"award-number":["32171428"]}]},{"name":"CAS Youth Interdisciplinary Team","award":["XDB0480000"],"award-info":[{"award-number":["XDB0480000"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Life"],"abstract":"<jats:p>Live-attenuated vaccines face a critical challenge in balancing immunogenicity with safety. To address this, we engineered programmable finite-replicated organisms (FROs) by depositing a limited number of indispensable components (such as noncanonical amino acids, ncAAs) within the cell, consuming the coenabling precise control of bacterial replication capability while preserving antigenic breadth. Two strategies were adopted to achieve the following purposes: (1) encoding ncAA in essential genes; (2) encoding ncAA in antitoxin of toxin\u2013antitoxin (TA) systems. As noncanonical amino acids, 3,5-dichlorotyrosine (Cl2Y) was encoded by the amber codon (TAG) and inserted into the essential genes (e.g., serS, murG, and dnaA) or antitoxin genes. After optimizing expression and the number of amber codons in the storage genes, the FRO cells can grow up to six generations, achieving amplification approaching 100 times after depletion of the ncAA in the growth medium. The escape frequencies are 10\u22125 to 10\u22127, which need to be optimized by combining multiple storage genes in the same genome in the future. This work holds the potential to amplify the amounts of antigens for vaccines, potentially accelerating the development of next-generation vaccines against antibiotic-resistant threats.<\/jats:p>","DOI":"10.3390\/life15091381","type":"journal-article","created":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T08:28:15Z","timestamp":1756715295000},"page":"1381","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A Programmable Finite-Replicated Organism Framework for Balanced Safety and Functionality"],"prefix":"10.3390","volume":"15","author":[{"given":"Mengyuan","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Green Biomanufacturing, MOE Key Lab. Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei","family":"Du","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4789-6516","authenticated-orcid":false,"given":"Fankang","family":"Meng","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenhui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Cell and Gene Circuit Design, State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanhui","family":"Xiang","sequence":"additional","affiliation":[{"name":"Center for Cell and Gene Circuit Design, State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiong","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Green Biomanufacturing, MOE Key Lab. Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunbo","family":"Lou","sequence":"additional","affiliation":[{"name":"Center for Cell and Gene Circuit Design, State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"4918","DOI":"10.1016\/j.vaccine.2023.06.074","article-title":"Development of toxin-antitoxin self-destructive bacteria, aimed for salmonella vaccination","volume":"41","author":"Gruzdev","year":"2023","journal-title":"Vaccine"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e03557-23","DOI":"10.1128\/spectrum.03557-23","article-title":"A novel vaccine strategy using quick and easy conversion of bacterial pathogens to unnatural amino acid-auxotrophic suicide derivatives","volume":"12","author":"Nagasawa","year":"2024","journal-title":"Microbiol. 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